de novo enzyme design using rosetta3使用rosetta3新创酶设计.pdf

De Novo Enzyme Design Using Rosetta3 1,2 3 1 1 1,2 Florian Richter *, Andrew Leaver-Fay , Sagar D. Khare , Sinisa Bjelic , David Baker 1 Department of Biochemistry, University of Washington, Seattle, Washington, United States of America, 2 Interdisciplinary Program in Biomolecular Structure and Design, University of Washington, Seattle, Washington, United States of America, 3 Department of Biochemistry, University of North Carolina, Chapel Hill, North Carolina, United States of America Abstract The Rosetta de novo enzyme design protocol has been used to design enzyme catalysts for a variety of chemical reactions, and in principle can be applied to any arbitrary chemical reaction of interest, The process has four stages: 1) choice of a catalytic mechanism and corresponding minimal model active site, 2) identification of sites in a set of scaffold proteins where this minimal active site can be realized, 3) optimization of the identities of the surrounding residues for stabilizing interactions with the transition state and primary catalytic residues, and 4) evaluation and ranking the resulting designed sequences. Stages two through four of this process can be carried out with the Rosetta package, while stage one needs to be done externally. Here, we demonstrate how to carry out the Rosetta enzyme design protocol from start to end in detail using for illustration the triosephosphate isomerase reaction. Citation: Richter F, Leaver-Fay A, Khare SD, Bjelic S, Baker D (2011) De Novo Enzyme Design Using Rosetta3. PLoS ONE 6(5): e19230. doi:10.1371/ journal.pone.0019230 Editor: Vladimir N. Uversky, University of South Florida College of Medicine, United States of America Received February 15, 2011; Accepted March 23, 2011; Published Ma